Is it not your path to the files? If I look at your file structure and the location of the files the path should be different. Also if you print your scalars you would notice that the $file_sec comes back different then expected. In your case it would result in:

$file: "/files/data.pri"
$file_sec: "/files/files/data.sec"

This should do what you want:

# mycode.pl

my $file     = "files/data.pri";

my $name     =  (split(/\./,$file))[0];
my $file_sec = "$name.sec";
[download]

prints now:

$file: "file/data.pri"
$file_sec: "file/data.sec"

hope this helps,

Critter